I’m a huge noob (i.e. I just started playing MvC2) but this is the team I’ve started with.
Hayato - I find him to be a solid point man who is fairly easy to combo with and launch with.
Iron Man (Alpha Assist) - I love his Proton Cannon and fighting with him if Hayato goes down is easy, but I’m not pulling off any infinites lol.
Cyclops (Beta Assist) - Love his hyper, launching is a bit tougher for me with him.
I just love this game though.
Rogue/Storm/Tron.
I’ve always loved Rogue and Storm as characters, and Tron assist is a god send to rushdown characters. Vegita-x was my inspiration for this team as well.
Cyclops, Cammy, and Mega Man…
Cyclops is my favorite X-Men. I have used Cammy she fits in good with Cyclops. Mega Man is real fun to play with and compliments this team…
Cable/CapCom/Ironman
I was using Cable/CapCom/Storm, but I seem to have a easier time with Ironman in there because his assist is faster. Cable’s gun into viper beam is annoying on it’s own, but add CapCom’s anti-air assist it becomes pretty hard to get in on me.
Team Scrub. Sent just feels so…right. And with capcom he is even better. It just flows for me.
Sent: My best char, I just love his combos and his super.
Strider: Liked him since I first played the game, got back into him and learned him now he is in my new team.
Doom: His assist, thats about it right now but I am working on getting good with him.
my team…
Hayato:
I love how his gameplay matches his style- Very smooth, calm, and stylish. If you don’t have any patience, stay away from this guy. His plasma combos suck IN the opponent whereas most character push them away when comboing. Very cool.
Rogue:
The heart and soul of my team. The first character I learned how to do aerial combos with. As soon as I saw a lvl 9 CPU play Rogue when she was the last character, I knew I had to learn to make my Rogue move like that.
Tron:
Ah, you know. Damage, damage, damage. Lunch Rush is incredible and she ties up the wackiness of the team nicely. She’s won me many, many matches by a crazy comeback when people underestimate her.
Cammy - Favorite Street Fighter Character
Cable - Pumps up the teams overall strength
Gambit - Favorite Marvel Character
Magneto Sentinel Tron Bonne because it can end a match very fast plus i love magneto in x-men and sentinel is my best and tron is just a cool character
my joke team is venom jugg and cyclops because those are sum of my favorite character
If I want to lose: Mag/IM/Locke
I just suck pretty bad with Mag but his speed makes him so fun.
Other then that: IM/Cable/Doom
BH/Cable/Cyke
Juggs/Tron/Doom
idk I play alot of random other characters as well although I am not really good with any of them.
I always loved Akuma, Spidey and wolverine thats my classic team since the past 10 years, and I still love em. But now im workin on these 3…
Akuma-Can air fireball downward, good rushdown and runaway and shun goku satsu and can land it pretty often, loved him since MSvSF.
Omega Red- just picked him up, havent used him since MSvsSF. Can control the area with long range grabs and can steal life force. Reminds me of a soul reaper or something like that which is cool. And good combos into throws does nice damage.
Hulk- Strong,Armor,and Gamma Crush with omega destroyer is 80% of your life. And some nice and strong combos if u use him rite. My favorite Big Guy since Marvel super heroes.
I am a diehard MSS player. I will run that team against any other squad, no matter how great the disadvantage.
In the beginning I thought the team had some uniqueness and wasn’t that popular. I didn’t realize the truth until I started going to majors.
I began using the team exclusively after watching Jmar beat Eddie Lee with it at ECC9. Eddie Lee is mad good, which made the win all the more impressive in my eyes. Getting inside and beating a team with excellent zoning/chipping options is hard, and if they can block really well it’s a nightmare. Eddie Lee had gdlk defense that set too.
Jmar got past all the swords, rocks, viper beams and grenades to win the set, and it was hard fought. Player Ability>counter teams.
Like all MSS players though, I play pretty much MS anything.
Blackheart/Doom/CapCom.
Blackheart is my favorite character in MVC2 and Doom is my favorite out of the Marvel Characters in MVC2. CapCom just sort of fits for strategic reasons. I think his assist looks pretty cool too I guess.
Morrigan - After trying out the entire cast, she’s the most fun character I’ve played. Plus I’ve been a fan of occult (particularly vampire) themed literature for a while (inb4twilight… seriously, I mean like Stoker-esque works, not garbage :P)
Tron - Mega Man is one of my all-time favorite series, and she’s the only representative of the series who doesn’t suck :P… Also she’s fun and her assists help out Morrigan 
Sonson - I have seen very few characters across any game as goofy as this one. She is the one character on my team I’m considering switching out, but the hilarity of running around the borders of the screen, throwing monkeys, and turning my opponents into watermelons is just too enticing to give up.
~SSCorT~ (Id recommend this starting team for anyone!)
Sentinal - Fly/Unfly is fun and can easily lock someone down with an assist
Storm - How she can gather super so quickly, the way almost all her moves/supers can be linked. Also because she is very fast and can usually punish other people easily.
Captain Commando - Just for his assist Links with almost anything.
T.Bone - The ridiculous amount of damage when she assists.
~MSP~
Magneto - Although I’m still learning he’s very fast and easy to mix people up with.
Storm - Same Reason Above
Psylocke - Her wonderful assist, not to mention she is still a great character to play with as well unlike cap or tbone.
!! 
when i had the game when i was like 8 or 9 megaman, bbhood, and cable.
now Jill- love ma zombies
tron- love ma servbot
doom- love me rockz
magneto(A), Sent. (Y), Psylocke (A)
Because I fucking suck with Storm, so I would prefer to use Sentinel. Has been that way for about 8 years, lol.
or
Magneto(A), Cable (B), Sent. (A)
because using the rocket-punch in a combo or reset with mags is too fucking good.
Hayato, Sakura, Strider
They are the three most fun characters in the game to me, and I like to get in people’s faces.
Megaman and Spider-man are always on my team for badass nostalgia reasons. Then depending on how I feel/who I’m playing, my third is Cable, Cyclops, or glitched Juggs.
i love doom cuz of his ass thrusters and cool taunt. cable because of his enormous “weapon” and akuma because i love doing airborne whirly kicks.